1. Field of the Invention
The present invention relates generally to gene regulatory networks and more specifically to identifying genomic sequences which function as cis-regulatory modules.
2. Background Information
In bilaterian animals, such as humans, all major life processes, both developmental and physiological, are controlled by large gene networks. The gene networks that control development are of particular importance, as well as of particular complexity. These networks define each bilaterian species and lade, and they determine the ultimate inherited capabilities of the organism, since by their hardwired architecture, they define all species-specific aspects of the body plan.
Whole genome analysis has demonstrated that the most important genes utilized in development are all shared across Bilateria. These genes are the genes encoding transcriptional factors and co-factors and elements of signaling systems. Differences in the repertoire of these genes, or of genomically encoded protein domains, cannot account for the differences in body plan amongst bilaterian animals: rather, the causal explanation for particular developmental pathways lies in the regulatory connections programmed in the genome.
But as detailed functional studies have revealed the internal structure of some cis-regulatory modules, it is less clear whether much of the sequence length that is included in the relatively conserved sequences must be located between, and not within, the known transcription factor target sites. It is unlikely that base pairs located between the transcription factor target sites of cis-regulatory modules have sequence dependent function, and the mechanism that constrains evolutionary change within cis-regulatory modules is incompletely understood.